def test_set_duplicate_stdout(self):
job = AbstractJob()
job.add_outputs(File("a"))
with pytest.raises(DuplicateError) as e:
job.set_stdout(File("a"))
assert "file: {file}".format(file=File("a")) in str(e)
def test_get_outputs(self):
job = AbstractJob()
f1 = File("a")
job.add_outputs(f1)
assert job.get_outputs() == {f1}
def test_add_outputs(self):
job = AbstractJob()
f1 = File("a")
f2 = File("b")
job.add_outputs(f1, f2)
assert job.get_outputs() == {f1, f2}
def test_add_inputs_and_outputs(self):
job = AbstractJob()
job.add_inputs(File("a"))
job.add_outputs(File("b"))
with pytest.raises(DuplicateError) as e:
job.add_inputs(File("b"))
assert "file: {file}".format(file=File("b")) in str(e)
def test_tojson(self):
j = AbstractJob(_id="aj", node_label="test")
j.set_stdin("stdin")
j.set_stdout("stdout")
j.set_stderr("stderr")
j.add_args("-i", File("f1"))
j.add_inputs(File("if1"), File("if2"))
j.add_outputs(File("of1"), File("of2"))
j.add_checkpoint(File("cpf"))
result = json.loads(json.dumps(j, cls=_CustomEncoder))
result["uses"] = sorted(result["uses"], key=lambda use: use["lfn"])
expected = {
"id":
"aj",
"nodeLabel":
"test",
"arguments": ["-i", "f1"],
"stdin":
"stdin",
"stdout":
"stdout",
"stderr":
"stderr",
"uses": [
{
"lfn": "stdin",
"type": "input"
},
{
"lfn": "if1",
"type": "input"
},
{
"lfn": "if2",
"type": "input"
},
{
"lfn": "stdout",
"type": "output",
"stageOut": True,
"registerReplica": False,
},
{
"lfn": "stderr",
"type": "output",
"stageOut": True,
"registerReplica": False,
},
{
"lfn": "of1",
"type": "output",
"stageOut": True,
"registerReplica": False,
},
{
"lfn": "of2",
"type": "output",
"stageOut": True,
"registerReplica": False,
},
{
"lfn": "cpf",
"type": "checkpoint",
"stageOut": True,
"registerReplica": False,
},
],
}
expected["uses"] = sorted(expected["uses"], key=lambda use: use["lfn"])
assert result == expected
def test_set_duplicate_stderr(self):
job = AbstractJob()
job.add_outputs(File("a"))
with pytest.raises(DuplicateError):
job.set_stderr(File("a"))
def test_add_invalid_output(self):
job = AbstractJob()
with pytest.raises(TypeError) as e:
job.add_outputs(123, "abc")
assert "invalid output_file: 123" in str(e)